| options {base} | R Documentation |
Allow the user to set and examine a variety of global options which affect the way in which R computes and displays its results.
options(...)
getOption(x)
.Options
... |
any options can be defined, using |
x |
a character string holding an option name. |
Invoking options() with no arguments returns a list with the
current values of the options. Note that not all options listed below
are set initially. To access the value of a single option, one should
use getOption("width"), e.g., rather than
options("width") which is a list of length one.
.Options also always contains the options() list (as a
pairlist, unsorted), for S compatibility. Assigning to it will make a
local copy and not change the original.
For getOption, the current value set for option x, or
NULL if the option is unset.
For options(), a list of all set options sorted by name. For
options(name), a list of length one containing the set value,
or NULL if it is unset. For uses setting one or more options,
a list with the previous values of the options changed (returned
invisibly).
add.smooth:typically logical, defaulting to
TRUE. Could also be set to an integer for specifying how
many (simulated) smooths should be added. This is currently only
used by plot.lm.
check.bounds:logical, defaulting to FALSE. If
true, a warning is produced whenever a
vector (atomic or list) is extended, by something
like x <- 1:3; x[5] <- 6.
continue:a non-empty string setting the prompt used for lines which continue over one line.
defaultPackages:the packages that are attached by
default when R starts up. Initially set from value of the
environment variable R_DEFAULT_PACKAGES, or if that is unset
to c("datasets", "utils", "grDevices", "graphics", "stats",
"methods"). (Set R_DEFAULT_PACKAGES to NULL or
a comma-separated list of package names.) A call to
options should be in your ‘.Rprofile’ file to ensure
that the change takes effect before the base package is
initialized (see Startup).
deparse.max.lines:controls the number of lines used
when deparsing in traceback and
browser. Initially unset, and only used if set to
a positive integer.
digits:controls the number of digits to print when
printing numeric values. It is a suggestion only. Valid values
are 1...22 with default 7. See the warning in
print.default about values greater than 15.
digits.secs:controls the maximum number of digits to
print when formatting time values in seconds. Valid values
are 0...6 with default 0. See strftime.
download.file.method:Method to be used for
download.file. Currently download methods
"internal", "wget" and "lynx" are available.
There is no default for this option, when method = "auto"
is chosen: see download.file.
echo:logical. Only used in non-interactive mode,
when it controls whether input is echoed. Command-line option
--slave sets this to FALSE, but otherwise
it starts the session as TRUE.
encoding:The name of an encoding, default
"native.enc"). See connections.
error:either a function or an expression governing
the handling of non-catastrophic errors such as those generated by
stop as well as by signals and internally detected
errors. If the option is a function, a call to that function,
with no arguments, is generated as the expression. The default
value is NULL: see stop for the behaviour in
that case. The functions dump.frames and
recover provide alternatives that allow post-mortem
debugging. Note that these need to specified as e.g.
options=utils::recover in startup files such as
‘.Rprofile’.
expressions:sets a limit on the number of nested
expressions that will be evaluated. Valid values are
25...500000 with default 5000. If you increase it, you may
also want to start R with a larger protection stack;
see --max-ppsize in Memory. Note too that
you may cause a segfault from overflow of the C stack, and on OSes
where it is possible you may want to increase that.
keep.source:When TRUE, the source code for
functions (newly defined or loaded) is stored in their
"source" attribute (see attr) allowing
comments to be kept in the right places.
The default is interactive(), i.e., TRUE for
interactive use.
keep.source.pkgs:As for keep.source, for
functions in packages loaded by library or
require. Defaults to FALSE unless the
environment variable R_KEEP_PKG_SOURCE is set to
yes.
Note this does not apply to packages using lazy-loading or saved images. Whether they have kept source is determined when they are installed (and is almost certainly false).
mailer:default mailer used by
bug.report(). Can be "none".
max.contour.segments:positive integer, defaulting to
250000 and usually not set. A limit on the number of
segments in a single contour line in contour or
contourLines.
max.print:integer, defaulting to 99999.
print or show methods can make use of
this option, to limit the amount of information that is printed,
to something in the order of (and typically slightly less than)
max.print entries.
OutDec:one-character string. The character to be
used as the decimal point in output conversions, that is in
printing, plotting and as.character but not deparsing.
pager:the command used for displaying text files by
file.show.
Defaults to ‘R_HOME/bin/pager’, which selects a pager
via the PAGER environment variable (and that usually
defaults to less).
Can be a character string or an R function, in which case it
needs to accept the same first four arguments as
file.show.
papersize:the default paper format used by
postscript; set by environment variable
R_PAPERSIZE when R is started: if that is unset or invalid
it defaults to
a value derived from the locale category LC_PAPER, or
if that is unavailable to a default set when R was built.
pdfviewer:default PDF viewer. The default is set from the environment variable R_PDFVIEWER.
printcmd:the command used by postscript
for printing; set by environment variable R_PRINTCMD when
R is started. This should be a command that expects either input
to be piped to ‘stdin’ or to be given a single filename
argument.
prompt:a non-empty string to be used for R's prompt;
should usually end in a blank (" ").
rl_word_breaks:Used for the readline-based terminal
interface. Default value " \t\n\"\\'`><=%;,|&\{()\}".
This is the set of characters use to break the input line up into
tokens for object- and file-name completion. Those who do not use
spaces around operators may prefer
" \t\n\"\\'`><=+-*%;,|&\{()\}".
which was the default in R 2.5.0. (The default in pre-2.5.0
versions of R was " \t\n\"\\'`@$><=;|&\{(".)
save.defaults, save.image.defaults:see save.
scipen:integer. A penalty to be applied
when deciding to print numeric values in fixed or exponential
notation. Positive values bias towards fixed and negative towards
scientific notation: fixed notation will be preferred unless it is
more than scipen digits wider.
showWarnCalls, showErrorCalls:a logical. Should warning and error messages show a summary of the call stack? By default error calls are shown in non-interactive sessions.
showNCalls:a integer. Controls how long the sequence of calls must be (in bytes) before ellipses are used. Defaults to 40 and should be at least 30 and no more than 500.
show.error.messages:a logical. Should error messages
be printed? Intended for use with try or a
user-installed error handler.
stringsAsFactors:The default setting for arguments of
data.frame and read.table.
texi2dvi:used by function
texi2dvi in package tools.
Set at startup from the environment variable R_TEXI2DVICMD.
timeout:integer. The timeout for some Internet
operations, in seconds. Default 60 seconds. See
download.file and connections.
topLevelEnvironment:see topenv and
sys.source.
useFancyQuotes:see sQuote.
verbose:logical. Should R report extra information
on progress? Set to TRUE by the command-line option
--verbose.
warn:sets the handling of warning messages. If
warn is negative all warnings are ignored. If warn
is zero (the default) warnings are stored until the top–level
function returns. If fewer than 10 warnings were signalled they
will be printed otherwise a message saying how many (max 50) were
signalled. An object called last.warning is
created and can be printed through the function
warnings. If warn is one, warnings are
printed as they occur. If warn is two or larger all
warnings are turned into errors.
warnEscapes:logical. If true (the default) the parser warns on unrecognized (backslash) escape sequences and there is a truncation warning on any attempt to create a character string containing an embedded nul.
warnPartialMatchArgs:logical. If true, warns if partial matching is used in argument matching.
warnPartialMatchAttr:logical. If true, warns if
partial matching is used in extracting attributes via
attr.
warnPartialMatchDollar:logical. If true, warns if
partial matching is used for extraction by $.
warning.expression:an R code expression to be called
if a warning is generated, replacing the standard message. If
non-null it is called irrespective of the value of option
warn.
warning.length:sets the truncation limit for error and warning messages. A non-negative integer, with allowed values 100...8170, default 1000.
width:controls the maximum number of columns on a
line used in printing vectors, matrices and arrays, and when
filling by cat.
Columns are normally the same as characters except in CJK languages.
You may want to change this if you re-size the window that R is running in. Valid values are 10...10000 with default normally 80. (The limits on valid values are in file ‘Print.h’ and can be changed by re-compiling R.) Some R consoles automatically change the value when they are resized.
The ‘factory-fresh’ default settings of some of these options are
add.smooth | TRUE |
check.bounds | FALSE |
continue | "+ " |
digits | 7 |
echo | TRUE |
encoding | "native.enc" |
error | NULL |
expressions | 5000 |
keep.source | interactive() |
keep.source.pkgs | FALSE |
max.print | 99999 |
OutDec | "." |
prompt | "> " |
scipen | 0 |
show.error.messages | TRUE |
timeout | 60 |
verbose | FALSE |
warn | 0 |
warnings.length | 1000 |
width | 80 |
Others are set from environment variables or are platform-dependent.
These will be set when package grDevices (or its name space) is loaded if not already set.
device:a character string giving
the name of a function, or the function object itself,
which when called creates a new graphics device of the default
type for that session. The value of this option defaults to the
normal screen device (e.g., X11, windows or
quartz) for an interactive session, and pdf
in batch use or if a screen is not available. If set to the name
of a device, the device is looked for first from the global
environment (that is down the usual search path) and then in the
grDevices namespace.
The default values in interactive and non-interactive sessions are configurable via environment variables R_INTERACTIVE_DEVICE and R_DEFAULT_DEVICE respectively.
locatorBell:logical. Should selection in locator
and identify be confirmed by a bell? Default TRUE.
Honoured at least on X11 and windows devices.
device.ask.default:logical. The default for
devAskNewPage("ask") when a device is opened.
bitmapType:character. The default type for the
bitmap devices such as png. Defaults to
"cairo" on systems where that is available, or to
"quartz" on Mac OS X where that is available.
These will be set when package stats (or its name space) is loaded if not already set.
contrasts:the default contrasts used in
model fitting such as with aov or lm.
A character vector of length two, the first giving the function to
be used with unordered factors and the second the function to be
used with ordered factors. By default the elements are named
c("unordered", "ordered"), but the names are unused.
na.action:the name of a function for treating missing
values (NA's) for certain situations.
show.coef.Pvalues:logical, affecting whether P
values are printed in summary tables of coefficients. See
printCoefmat.
show.signif.stars:logical, should stars be printed on
summary tables of coefficients? See printCoefmat.
ts.eps:the relative tolerance for certain time series
(ts) computations. Default 1e-05.
ts.S.compat:logical. Used to select S compatibility
for plotting time-series spectra. See the description of argument
log in plot.spec.
These will be set when package utils (or its name space) is loaded if not already set.
browser:default HTML browser used by
help.start() and browseURL on UNIX, or
a non-default browser on Windows. Alternatively, an R function that
is called with a URL as its argument.
de.cellwidth:integer: the cell widths (number of
characters) to be used in the data editor dataentry.
If this is unset (the default), 0, negative or NA, variable
cell widths are used.
demo.ask:default for the ask argument of
demo.
editor:a non-empty string, or a function that is
called with a file path as argument.
Sets the default text editor, e.g., for
edit. Set from the environment variable
VISUAL on UNIX.
example.ask:default for the ask argument of
example.
help.try.all.packages:default for an argument of
help.
HTTPUserAgent:string used as the user agent in HTTP
requests. If NULL, HTTP requests will be made without a
user agent header. The default is R (<version> <platform>
<arch> <os>)
internet.info:The minimum level of information to be printed on URL downloads etc. Default is 2, for failure causes. Set to 1 or 0 to get more information.
menu.graphics:Logical: should graphical menus be
used if available?. Defaults to TRUE. Currently applies
to chooseCRANmirror, setRepositories
and to select from multiple help files in help.
pkgType:The default type of packages to be downloaded
and installed – see install.packages.
Possible values are "source" (the default except under the
CRAN Mac OS X build) and "mac.binary". The latter can
have a suffix if supported by a special build, such as
"mac.binary.leopard" to access the "leopard" tree
of repositories instead of the default "universal".
repos:URLs of the repositories for use by
update.packages. Defaults to
c(CRAN="@CRAN@"), a value that causes some utilities to
prompt for a CRAN mirror. To avoid this do set the CRAN mirror,
by something like
local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cran";
options(repos=r)}).
Note that you can add more repositories (Bioconductor and
Omegahat, notably) using setRepositories().
SweaveHooks, SweaveSyntax:see Sweave.
unzip:a character string, the path of the command
used for unzipping help files, or "internal".
Defaults to the value of R_UNZIPCMD, which is set in
‘etc/Renviron’ if an unzip command was found during
configuration.
These will be "" if no suitable path is known.
latexcmd, dvipscmd:character strings giving commands to be used in off-line printing of help pages.
Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth & Brooks/Cole.
op <- options(); utils::str(op) # op() may contain functions.
getOption("width") == options()$width # the latter needs more memory
options(digits = 15)
pi
# set the editor, and save previous value
old.o <- options(editor = "nedit")
old.o
options(check.bounds = TRUE, warn = 1)
x <- NULL; x[4] <- "yes" # gives a warning
options(digits=5)
print(1e5)
options(scipen=3); print(1e5)
options(op) # reset (all) initial options
options("digits")
## Not run: ## set contrast handling to be like S
options(contrasts = c("contr.helmert", "contr.poly"))
## End(Not run)
## Not run: ## on error, terminate the R session with error status 66
options(error = quote(q("no", status=66, runLast=FALSE)))
stop("test it")
## End(Not run)
## Not run: ## Set error actions for debugging:
## enter browser on error, see ?recover:
options(error = recover)
## allows to call debugger() afterwards, see ?debugger:
options(error = dump.frames)
## A possible setting for non-interactive sessions
options(error = quote({dump.frames(to.file=TRUE); q()}))
## End(Not run)